6z25

From Proteopedia

Acylenzyme complex of ceftazidime bound to deacylation mutant KPC-4 (E166Q)

PDB ID 6z25

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Structural highlights

6z25 is a 1 chain structure with sequence from Klebsiella pneumoniae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.24Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BLKPC_KLEPN Hydrolyzes carbapenems, penicillins, cephalosporins and monobactams with varying efficiency.

Publication Abstract from PubMed

Class A serine beta-lactamases (SBLs) are key antibiotic resistance determinants in Gram-negative bacteria. SBLs neutralize beta-lactams via a hydrolytically labile covalent acyl-enzyme intermediate. Klebsiella pneumoniae carbapenemase (KPC) is a widespread SBL that hydrolyzes carbapenems, the most potent beta-lactams; known KPC variants differ in turnover of expanded-spectrum oxyimino-cephalosporins (ESOCs), e.g. cefotaxime and ceftazidime. Here, we compare ESOC hydrolysis by the parent enzyme KPC-2 and its clinically observed double variant (P104R/V240G) KPC-4. Kinetic analyses show KPC-2 hydrolyzes cefotaxime more efficiently than the bulkier ceftazidime, with improved ESOC turnover by KPC-4 resulting from enhanced turnover (kcat), rather than binding (KM). High-resolution crystal structures of ESOC acyl-enzyme complexes with deacylation-deficient (E166Q) KPC-2 and KPC-4 mutants show that ceftazidime acylation causes rearrangement of three loops; the Omega-, 240- and 270-loops, that border the active site. However, these rearrangements are less pronounced in the KPC-4 than the KPC-2 ceftazidime acyl-enzyme, and are not observed in the KPC-2:cefotaxime acyl-enzyme. Molecular dynamics simulations of KPC:ceftazidime acyl-enyzmes reveal that the deacylation general base E166, located on the Omega-loop, adopts two distinct conformations in KPC-2, either pointing 'in' or 'out' of the active site; with only the 'in' form compatible with deacylation. The 'out' conformation was not sampled in the KPC-4 acyl-enzyme, indicating that efficient ESOC breakdown is dependent upon the ordering and conformation of the KPC Omega-loop. The results explain how point mutations expand the activity spectrum of the clinically important KPC SBLs to include ESOCs through their effects on the conformational dynamics of the acyl-enzyme intermediate.

Natural variants modify Klebsiella pneumoniae carbapenemase (KPC) acyl-enzyme conformational dynamics to extend antibiotic resistance.,Tooke CL, Hinchliffe P, Bonomo RA, Schofield CJ, Mulholland AJ, Spencer J J Biol Chem. 2020 Nov 30. pii: RA120.016461. doi: 10.1074/jbc.RA120.016461. PMID:33257320^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Tooke CL, Hinchliffe P, Bonomo RA, Schofield CJ, Mulholland AJ, Spencer J. Natural variants modify Klebsiella pneumoniae carbapenemase (KPC) acyl-enzyme conformational dynamics to extend antibiotic resistance. J Biol Chem. 2020 Nov 30. pii: RA120.016461. doi: 10.1074/jbc.RA120.016461. PMID:33257320 doi:http://dx.doi.org/10.1074/jbc.RA120.016461